Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, Scaevola taccada and S. hainanensis—Insight into Adaptation Outside of the Common Range
Abstract
:1. Introduction
2. Results
2.1. Genome Assembly and Annotation
2.2. Whole Genome Duplication and LTR Retrotransposon Insertion
2.3. Phylogeny Construction and Gene Copy Number Evolution
2.4. Genes under Positive Selection
2.5. Evolution of the FAR1 Gene Family in S. taccada and S. hainanensis
3. Discussion
4. Material and Methods
4.1. Plant Material
4.2. 10× Genomics Sequencing
4.3. Hi-C Sequencing
4.4. Short-Read Sequencing
4.5. De Novo Genome Assembling
4.6. Genome Annotation
4.7. Collinearity Analysis and Whole-Genome Duplication (WGD) Analysis
4.8. Phylogeny Construction and Divergence Time Estimation
4.9. Gene Group Evolution and Positive Selection Detection
4.10. Analyses of the FAR1 Gene Family
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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S. taccada | S. hainanensis | |
---|---|---|
Assembly summary (Scaffold length ≥ 10 kb) | ||
Number of scaffolds | 430 | 1014 |
Total length (bp) | 1,011,548,119 | 1,141,139,833 |
GC content (%) | 34.78% | 32.71% |
N50 (scaffolds) (bp) | 124,591,045 | 143,667,403 |
N90 (scaffolds) (bp) | 92,220,726 | 106,356,671 |
No. of scaffolds ≥ N50 | 4 | 4 |
No. of scaffolds ≥ N90 | 8 | 8 |
BUSCO evaluation of genome assembly | ||
Complete BUSCOs | 1525 (94.49%) | 1514 (93.80%) |
Single-copy BUSCOs | 1510 (93.56%) | 1485 (92.01%) |
Duplicated BUSCOs | 15 (0.93%) | 29 (1.80%) |
Fragmented BUSCOs | 40 (2.48%) | 41 (2.54%) |
Missing BUSCOs | 49 (3.04%) | 59 (3.66%) |
BUSCO evaluation of predicted gene models | ||
Complete BUSCOs | 1878 (88.5%) | 1974 (93.1%) |
Single-copy BUSCOs | 1844 (86.9%) | 1922 (90.6%) |
Duplicated BUSCOs | 34 (1.6%) | 52 (2.5%) |
Fragmented BUSCOs | 78 (3.7%) | 57 (2.7%) |
Fragmented BUSCOs | 165 (7.8%) | 90 (4.2%) |
Annotation summary | ||
Number of genes | 34,560 | 34,033 |
Mean gene length (bp) | 2949 | 2902 |
Mean exon length (bp) | 218 | 228 |
Mean exon counts per gene | 4.7 | 4.6 |
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Li, S.; Mao, X.; He, Z.; Xu, S.; Guo, Z.; Shi, S. Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, Scaevola taccada and S. hainanensis—Insight into Adaptation Outside of the Common Range. Int. J. Mol. Sci. 2023, 24, 7355. https://doi.org/10.3390/ijms24087355
Li S, Mao X, He Z, Xu S, Guo Z, Shi S. Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, Scaevola taccada and S. hainanensis—Insight into Adaptation Outside of the Common Range. International Journal of Molecular Sciences. 2023; 24(8):7355. https://doi.org/10.3390/ijms24087355
Chicago/Turabian StyleLi, Sen, Xiaomeng Mao, Ziwen He, Shaohua Xu, Zixiao Guo, and Suhua Shi. 2023. "Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, Scaevola taccada and S. hainanensis—Insight into Adaptation Outside of the Common Range" International Journal of Molecular Sciences 24, no. 8: 7355. https://doi.org/10.3390/ijms24087355